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Membrane protein/transport protein PDB id
2gif
Jmol
Contents
Protein chains
1032 a.a. *
Ligands
FLC ×2
* Residue conservation analysis
PDB id:
2gif
Name: Membrane protein/transport protein
Title: Asymmetric structure of trimeric acrb from escherichia coli
Structure: Acriflavine resistance protein b. Chain: a, b, c. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: acrb, acre. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Trimer (from PQS)
Resolution:
2.90Å     R-factor:   0.228     R-free:   0.267
Authors: M.A.Seeger,A.Schiefner,T.Eicher,F.Verrey,K.Diederichs,K.M.Po
Key ref:
M.A.Seeger et al. (2006). Structural asymmetry of AcrB trimer suggests a peristaltic pump mechanism. Science, 313, 1295-1298. PubMed id: 16946072 DOI: 10.1126/science.1131542
Date:
28-Mar-06     Release date:   12-Sep-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P31224  (ACRB_ECOLI) -  Multidrug efflux pump subunit AcrB
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1049 a.a.
1032 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   4 terms 
  Biological process     transport   4 terms 
  Biochemical function     transporter activity     4 terms  

 

 
DOI no: 10.1126/science.1131542 Science 313:1295-1298 (2006)
PubMed id: 16946072  
 
 
Structural asymmetry of AcrB trimer suggests a peristaltic pump mechanism.
M.A.Seeger, A.Schiefner, T.Eicher, F.Verrey, K.Diederichs, K.M.Pos.
 
  ABSTRACT  
 
The AcrA/AcrB/TolC complex spans the inner and outer membranes of Escherichia coli and serves as its major drug-resistance pump. Driven by the proton motive force, it mediates the efflux of bile salts, detergents, organic solvents, and many structurally unrelated antibiotics. Here, we report a crystallographic structure of trimeric AcrB determined at 2.9 and 3.0 angstrom resolution in space groups that allow asymmetry of the monomers. This structure reveals three different monomer conformations representing consecutive states in a transport cycle. The structural data imply an alternating access mechanism and a novel peristaltic mode of drug transport by this type of transporter.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Main structural differences of the AcrB monomers. (A) The three AcrB monomers shown in top view as cylinder presentation in blue (L), yellow (T), and red (O) are superimposed onto the symmetric AcrB trimer model depicted in transparent gray. In the T monomer (yellow), a hydrophobic pocket is defined by phenylalanines 136, 178, 610, 615, 617, and 628; valines 139 and 612; isoleucines 277 and 626; and tyrosine 327 at the PN2/PC1 interface. (B) Structural changes in the putative proton translocation site. Conserved residues D407, D408 (TM4), and K940 (TM10) in the three monomers (L, blue; T, yellow; O, red) are depicted with 2Fo-Fc electron density maps contoured at 0.5 (L) or 1 (T and O) as viewed from the cytoplasm. In the L and T monomers, the same conformation is observed, whereas in the O monomer, K940 forms a salt bridge with D407. This interaction seems to be stabilized by hydrogen bonding of T978 (TM11). To restore the geometry as it appears in the L monomer, proton uptake is anticipated.
Figure 3.
Fig. 3. Schematic representation of the AcrB alternating site functional rotation transport mechanism. The conformational states loose (L), tight (T), and open (O) are colored blue, yellow and red, respectively. (A) Side-view schematic representation of two of the three monomers of the AcrB trimer. AcrA and TolC are indicated in light green and light purple colors, respectively. The proposed proton translocation site (D407, D408, and K940) is indicated in the membrane part of each monomer. (B) The lateral grooves in the L and T monomer indicate the substrate binding sites. The different geometric forms reflect low (triangle), high (rectangle), or no (circle) binding affinity for the transported substrates. The PN1 subdomains (including the pore helices) located in the middle of the model are highlighted and form the corners of an asymmetric triangle (white) to indicate the communication between the monomers. In the first state of the cycle, a monomer binds a substrate (acridine) in its transmembrane domain (L conformation), subsequently transports the substrate from the transmembrane domain to the hydrophobic binding pocket (conversion to T conformation) and finally releases the substrate in the funnel toward TolC (O conformation). The conversion from the O-monomer to the L-monomer conformation is suggested to be the major energy-requiring (proton motive force–dependent) step in this functional rotation cycle and requires the binding of a proton to the proton translocation site (D407, D408, and K940) from the periplasm. The conversion from the T monomer to the O monomer is accompanied by the release of a proton from the proton translocation site to the cytoplasm. AcrA can be expected to participate in the transduction of the conformational changes from AcrB to TolC, which results in the opening of the TolC channel and the facilitation of drug extrusion to the outside of the cell.
 
  The above figures are reprinted by permission from the AAAs: Science (2006, 313, 1295-1298) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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PDB code: 3ne5
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A single acidic residue can guide binding site selection but does not govern QacR cationic-drug affinity.
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PDB code: 3pm1
21296164 N.Monroe, G.Sennhauser, M.A.Seeger, C.Briand, and M.G.Grütter (2011).
Designed ankyrin repeat protein binders for the crystallization of AcrB: Plasticity of the dominant interface.
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PDB codes: 3noc 3nog
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Structures of the multidrug exporter AcrB reveal a proximal multisite drug-binding pocket.
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PDB codes: 3aoa 3aob 3aoc 3aod
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Structures of sequential open states in a symmetrical opening transition of the TolC exit duct.
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PDB codes: 2wmz 2xmn
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Metal-induced conformational changes in ZneB suggest an active role of membrane fusion proteins in efflux resistance systems.
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PDB code: 3lnn
20804453 F.Husain, and H.Nikaido (2010).
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20865003 F.Long, C.C.Su, M.T.Zimmermann, S.E.Boyken, K.R.Rajashankar, R.L.Jernigan, and E.W.Yu (2010).
Crystal structures of the CusA efflux pump suggest methionine-mediated metal transport.
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PDB codes: 3k07 3kso 3kss
20399187 G.Phan, H.Benabdelhak, M.B.Lascombe, P.Benas, S.Rety, M.Picard, A.Ducruix, C.Etchebest, and I.Broutin (2010).
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PDB code: 3d5k
20038594 H.S.Kim, D.Nagore, and H.Nikaido (2010).
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20606071 J.A.Bohnert, B.Karamian, and H.Nikaido (2010).
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20132445 J.W.Weeks, T.Celaya-Kolb, S.Pecora, and R.Misra (2010).
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19961541 R.Ernst, P.Kueppers, J.Stindt, K.Kuchler, and L.Schmitt (2010).
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20548943 R.Schulz, A.V.Vargiu, F.Collu, U.Kleinekathöfer, and P.Ruggerone (2010).
Functional rotation of the transporter AcrB: insights into drug extrusion from simulations.
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Site-directed disulfide cross-linking to probe conformational changes of a transporter during its functional cycle: Escherichia coli AcrB multidrug exporter as an example.
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19695261 C.C.Su, F.Yang, F.Long, D.Reyon, M.D.Routh, D.W.Kuo, A.K.Mokhtari, J.D.Van Ornam, K.L.Rabe, J.A.Hoy, Y.J.Lee, K.R.Rajashankar, and E.W.Yu (2009).
Crystal structure of the membrane fusion protein CusB from Escherichia coli.
  J Mol Biol, 393, 342-355.
PDB codes: 3h94 3h9i 3h9t 3ooc 3opo 3ow7
18936189 C.Wehmeier, S.Schuster, E.Fähnrich, W.V.Kern, and J.A.Bohnert (2009).
Site-directed mutagenesis reveals amino acid residues in the Escherichia coli RND efflux pump AcrB that confer macrolide resistance.
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19219012 E.Schleiff, and R.Tampé (2009).
Membrane proteins take center stage in Frankfurt.
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19136595 H.I.Zgurskaya (2009).
Covalently linked AcrB giant offers a new powerful tool for mechanistic analysis of multidrug efflux in bacteria.
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19722844 H.I.Zgurskaya (2009).
Multicomponent drug efflux complexes: architecture and mechanism of assembly.
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19026770 H.Nikaido, and Y.Takatsuka (2009).
Mechanisms of RND multidrug efflux pumps.
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Multidrug resistance in bacteria.
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MacB ABC Transporter Is a Dimer Whose ATPase Activity and Macrolide-binding Capacity Are Regulated by the Membrane Fusion Protein MacA.
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CzcP is a novel efflux system contributing to transition metal resistance in Cupriavidus metallidurans CH34.
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19416927 K.M.Pos (2009).
Trinity revealed: Stoichiometric complex assembly of a bacterial multidrug efflux pump.
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19307562 K.Nagano, and H.Nikaido (2009).
Kinetic behavior of the major multidrug efflux pump AcrB of Escherichia coli.
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19258536 L.Cuthbertson, I.L.Mainprize, J.H.Naismith, and C.Whitfield (2009).
Pivotal roles of the outer membrane polysaccharide export and polysaccharide copolymerase protein families in export of extracellular polysaccharides in gram-negative bacteria.
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The assembled structure of a complete tripartite bacterial multidrug efflux pump.
  Proc Natl Acad Sci U S A, 106, 7173-7178.
PDB code: 2v4d
19578383 N.P.Barrera, S.C.Isaacson, M.Zhou, V.N.Bavro, A.Welch, T.A.Schaedler, M.A.Seeger, R.N.Miguel, V.M.Korkhov, H.W.van Veen, H.Venter, A.R.Walmsley, C.G.Tate, and C.V.Robinson (2009).
Mass spectrometry of membrane transporters reveals subunit stoichiometry and interactions.
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19451626 N.Tal, and S.Schuldiner (2009).
A coordinated network of transporters with overlapping specificities provides a robust survival strategy.
  Proc Natl Acad Sci U S A, 106, 9051-9056.  
19433508 P.H.Lee, K.L.Kuo, P.Y.Chu, E.M.Liu, and J.H.Lin (2009).
SLITHER: a web server for generating contiguous conformations of substrate molecules entering into deep active sites of proteins or migrating through channels in membrane transporters.
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19426128 R.Krämer, and C.Ziegler (2009).
Regulative interactions of the osmosensing C-terminal domain in the trimeric glycine betaine transporter BetP from Corynebacterium glutamicum.
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19289182 R.Misra, and V.N.Bavro (2009).
Assembly and transport mechanism of tripartite drug efflux systems.
  Biochim Biophys Acta, 1794, 817-825.  
19383457 R.Schulz, and U.Kleinekathöfer (2009).
Transitions between closed and open conformations of TolC: the effects of ions in simulations.
  Biophys J, 96, 3116-3125.  
19453279 T.Eicher, L.Brandstätter, and K.M.Pos (2009).
Structural and functional aspects of the multidrug efflux pump AcrB.
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19678712 X.Z.Li, and H.Nikaido (2009).
Efflux-mediated drug resistance in bacteria: an update.
  Drugs, 69, 1555-1623.  
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Covalently linked trimer of the AcrB multidrug efflux pump provides support for the functional rotating mechanism.
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19788177 Z.Ma, F.E.Jacobsen, and D.P.Giedroc (2009).
Coordination chemistry of bacterial metal transport and sensing.
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Structure, function, and evolution of bacterial ATP-binding cassette systems.
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17729275 A.Rath, and C.M.Deber (2008).
Surface recognition elements of membrane protein oligomerization.
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  18931428 D.Veesler, S.Blangy, C.Cambillau, and G.Sciara (2008).
There is a baby in the bath water: AcrB contamination is a major problem in membrane-protein crystallization.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 880-885.
PDB code: 3d9b
18024521 G.Krishnamoorthy, E.B.Tikhonova, and H.I.Zgurskaya (2008).
Fitting periplasmic membrane fusion proteins to inner membrane transporters: mutations that enable Escherichia coli AcrA to function with Pseudomonas aeruginosa MexB.
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18805970 H.Yamanaka, H.Kobayashi, E.Takahashi, and K.Okamoto (2008).
MacAB is involved in the secretion of Escherichia coli heat-stable enterotoxin II.
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Direct metal transfer between periplasmic proteins identifies a bacterial copper chaperone.
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18389081 I.Bunikis, K.Denker, Y.Ostberg, C.Andersen, R.Benz, and S.Bergström (2008).
An RND-type efflux system in Borrelia burgdorferi is involved in virulence and resistance to antimicrobial compounds.
  PLoS Pathog, 4, e1000009.  
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Site-directed mutagenesis reveals putative substrate binding residues in the Escherichia coli RND efflux pump AcrB.
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Gating at both ends and breathing in the middle: conformational dynamics of TolC.
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PDB code: 3ech
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PDB codes: 2vdd 2vde
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PDB code: 2i6w
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PDB code: 2j8s
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PDB code: 2rdd
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Structural biology: the ins and outs of drug transport.
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The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.